erikm at xray.bmc.uu.se
Thu Jan 28 16:03:50 CET 2010
afsaneh maleki skrev:
> thanks dear justin'
> it is right that the output of the analysis tools generally writes
> axis labels and data set legends. in hblife.xyg file is written that
> x axis label "Time (ps)" and the last time is written 14300.001
> whereas my simulated time is 40000 ps not 143000.00 ps
> i send you this file
I don't remember the details about the calculation of lifetimes, but I
believe it's an estimate of how the half lifes of hydrogen bonds. You
can also get this quantity, along with the kinetic constants and
energies for hb breaking and frormation, using -ac. If I remember
correctly, -ac uses a more reliable method.
> Best wishes,
> On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> afsaneh maleki wrote:
> would you please elaborate the first column in the hblife.xvg
> hblife.xyg is the output of the following command:
> g_hbond -life hblife.xvg
> this column don't show the real time in simulated system.what
> are these times?
> Check the headers in the .xvg file; the output of the analysis
> tools generally writes axis labels and data set legends. If it
> still doesn't make sense, post a snippet of your file.
> thanks in advance,
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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